Skirmantas Kriaucionis and Nathaniel Heintz found a new piece of DNA's genetic code and energized the field of epigenetics research.

Relying on old-fashioned techniques allowed these researchers to make a surprising discovery.

The history of science glitters with accidental discoveries, from Roentgen's x-rays to Fleming's penicillin. And despite what some would consider a creeping loss of flexibility in the modern scientific process, researchers from time to time still stumble across something truly surprising. Just ask HHMI investigator Nathaniel Heintz and his postdoctoral associate Skirmantas Kriaucionis.

Their serendipitous finding of a DNA constituent called hydroxymethylcytosine—roughly akin to the discovery of a new letter of the AGCT genetic code—has energized the fast-growing field of epigenetics, the study of the all-important mechanisms that maintain genes in an “on” or “off” state within cells.

“Our finding of this nucleotide in animal cells was completely unexpected,” says Heintz, whose lab is based at Rockefeller University in New York City.

It began with a dark spot on a glass chromatography plate—a spot that shouldn't have been there. Under Heintz's guidance, Kriaucionis had been trying to measure levels of a known epigenetic marker, a gene-silencing nucleotide known as methylcytosine (mC), in a sample of DNA from mouse Purkinje cells.

These large neurons, located in the movement-coordinating cerebellum, are difficult to harvest in large quantities, says Heintz: “To get enough DNA to do the analysis was difficult, so we used a very sensitive, old-fashioned methodology for detecting DNA nucleotides.”

The experiment yielded a chromatogram, in which separate spots of clustered material indicate the presence of unique DNA nucleotides within the sample. But near the expected spot for mC Kriaucionis saw another spot in a surprising location, suggesting an unknown nucleotide.

Was it an experimental artifact? “We were suspicious,” Kriaucionis remembers. After searching the literature and repeating the experiment numerous times with different controls, however, the researchers realized that the mystery spot marked a nucleotide known as hydroxymethylcytosine (hmC). Previously, hmC had been considered a rare DNA modification found only in primitive, bacteria-infecting viruses. Its relative abundance in a mammalian brain cell strongly suggested that it could be a major epigenetic player.

Photo: Elizabeth Weinberg

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